AutoCloner

Multiple sequence alignment - TraesCS2B01G488300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS2B01G488300	chr2B	100.000	2366	0	0	1	2366	685604585	685606950	0.000000e+00	4370.0
1	TraesCS2B01G488300	chr2B	92.454	2412	103	25	6	2366	686448738	686451121	0.000000e+00	3373.0
2	TraesCS2B01G488300	chr2B	87.070	1307	78	52	461	1721	685762681	685763942	0.000000e+00	1393.0
3	TraesCS2B01G488300	chr2B	89.404	755	62	13	719	1465	685279771	685280515	0.000000e+00	935.0
4	TraesCS2B01G488300	chr2B	81.917	1106	111	45	658	1726	686342799	686343852	0.000000e+00	852.0
5	TraesCS2B01G488300	chr2B	86.091	417	48	8	959	1367	685502825	685503239	7.760000e-120	440.0
6	TraesCS2B01G488300	chr2B	85.851	417	49	8	959	1367	685518107	685518521	3.610000e-118	435.0
7	TraesCS2B01G488300	chr2B	88.825	349	37	2	1025	1372	686808284	686808631	6.040000e-116	427.0
8	TraesCS2B01G488300	chr2B	91.129	248	11	4	380	617	686291831	686292077	2.270000e-85	326.0
9	TraesCS2B01G488300	chr2B	87.055	309	12	13	323	613	685277587	685277885	8.160000e-85	324.0
10	TraesCS2B01G488300	chr2B	90.726	248	12	4	380	617	686290726	686290972	1.060000e-83	320.0
11	TraesCS2B01G488300	chr2B	89.552	201	18	3	100	299	685762433	685762631	3.900000e-63	252.0
12	TraesCS2B01G488300	chr2B	90.960	177	14	2	16	191	685277364	685277539	1.090000e-58	237.0
13	TraesCS2B01G488300	chr2B	84.000	275	13	10	1465	1721	685280596	685280857	3.930000e-58	235.0
14	TraesCS2B01G488300	chr2B	83.333	198	29	3	2153	2347	799580129	799580325	1.870000e-41	180.0
15	TraesCS2B01G488300	chr2B	83.333	198	29	3	2153	2347	799582789	799582985	1.870000e-41	180.0
16	TraesCS2B01G488300	chr2B	94.737	38	1	1	349	385	686290681	686290718	9.130000e-05	58.4
17	TraesCS2B01G488300	chr2B	100.000	31	0	0	349	379	686291786	686291816	9.130000e-05	58.4
18	TraesCS2B01G488300	chr2A	91.712	1279	63	15	464	1726	711020738	711021989	0.000000e+00	1735.0
19	TraesCS2B01G488300	chr2A	92.308	663	30	9	1	645	710961729	710962388	0.000000e+00	922.0
20	TraesCS2B01G488300	chr2A	84.989	473	47	7	1896	2366	711022057	711022507	2.140000e-125	459.0
21	TraesCS2B01G488300	chr2A	85.788	387	53	2	983	1368	711033134	711033519	2.190000e-110	409.0
22	TraesCS2B01G488300	chr2A	84.463	354	38	14	643	987	710963699	710964044	1.360000e-87	333.0
23	TraesCS2B01G488300	chr2A	90.909	165	13	2	27	190	711020389	711020552	1.100000e-53	220.0
24	TraesCS2B01G488300	chr2A	85.124	121	1	7	323	426	711020621	711020741	8.940000e-20	108.0
25	TraesCS2B01G488300	chr2A	88.235	68	8	0	1726	1793	711033436	711033503	5.420000e-12	82.4
26	TraesCS2B01G488300	chr6B	82.791	215	33	3	2155	2366	555839463	555839250	3.100000e-44	189.0
27	TraesCS2B01G488300	chr2D	83.010	206	30	4	2155	2357	529667425	529667628	5.190000e-42	182.0
28	TraesCS2B01G488300	chr4D	82.843	204	32	3	2155	2358	498198435	498198635	1.870000e-41	180.0
29	TraesCS2B01G488300	chr3B	82.028	217	31	6	2154	2366	648893891	648893679	6.720000e-41	178.0
30	TraesCS2B01G488300	chr3D	82.028	217	29	9	2154	2366	414777492	414777702	2.420000e-40	176.0
31	TraesCS2B01G488300	chr3D	82.126	207	31	3	2158	2364	580980391	580980191	3.130000e-39	172.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS2B01G488300	chr2B	685604585	685606950	2365	False	4370.00	4370	100.00000	1	2366	1	chr2B.!!$F3	2365
1	TraesCS2B01G488300	chr2B	686448738	686451121	2383	False	3373.00	3373	92.45400	6	2366	1	chr2B.!!$F5	2360
2	TraesCS2B01G488300	chr2B	686342799	686343852	1053	False	852.00	852	81.91700	658	1726	1	chr2B.!!$F4	1068
3	TraesCS2B01G488300	chr2B	685762433	685763942	1509	False	822.50	1393	88.31100	100	1721	2	chr2B.!!$F8	1621
4	TraesCS2B01G488300	chr2B	685277364	685280857	3493	False	432.75	935	87.85475	16	1721	4	chr2B.!!$F7	1705
5	TraesCS2B01G488300	chr2A	711020389	711022507	2118	False	630.50	1735	88.18350	27	2366	4	chr2A.!!$F2	2339
6	TraesCS2B01G488300	chr2A	710961729	710964044	2315	False	627.50	922	88.38550	1	987	2	chr2A.!!$F1	986

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
87	88	0.323725	ACCCTGTGTGCCAATCATCC	60.324	55.0	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1889	5251	0.316937	AATGAAACTGCGCACACACG	60.317	50.0	5.66	0.0	0.0	4.49	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	4.021229	TGTTGACTATCATACTCGGGTGT	58.979	43.478	0.00	0.00	0.00	4.16
87	88	0.323725	ACCCTGTGTGCCAATCATCC	60.324	55.000	0.00	0.00	0.00	3.51
99	100	2.819984	AATCATCCTTGGCCACGCGT	62.820	55.000	3.88	5.58	0.00	6.01
107	108	0.885150	TTGGCCACGCGTCATAAACA	60.885	50.000	9.86	0.00	0.00	2.83
1203	4431	3.704566	TCTTGTACTACGGCATCCTCATT	59.295	43.478	0.00	0.00	0.00	2.57
1458	4686	5.513233	ACCATTTGCTTCCATCTGTTATCT	58.487	37.500	0.00	0.00	0.00	1.98
1522	4838	3.640029	ACGGAGAGTTTCAGGTTCTGTTA	59.360	43.478	0.00	0.00	32.61	2.41
1523	4839	4.238514	CGGAGAGTTTCAGGTTCTGTTAG	58.761	47.826	0.00	0.00	32.61	2.34
1524	4840	4.570930	GGAGAGTTTCAGGTTCTGTTAGG	58.429	47.826	0.00	0.00	32.61	2.69
1525	4841	4.283722	GGAGAGTTTCAGGTTCTGTTAGGA	59.716	45.833	0.00	0.00	32.61	2.94
1526	4842	5.474825	GAGAGTTTCAGGTTCTGTTAGGAG	58.525	45.833	0.00	0.00	32.61	3.69
1527	4843	5.148502	AGAGTTTCAGGTTCTGTTAGGAGA	58.851	41.667	0.00	0.00	32.61	3.71
1528	4844	5.782845	AGAGTTTCAGGTTCTGTTAGGAGAT	59.217	40.000	0.00	0.00	32.61	2.75
1577	4893	5.181009	TGCTTTCTGATCGATGTGAGATTT	58.819	37.500	0.54	0.00	0.00	2.17
1593	4909	6.944290	TGTGAGATTTTCATTGATCTGGTCTT	59.056	34.615	0.00	0.00	38.29	3.01
1658	4980	6.434028	CACATATTTGTTCCCCTCTCAGAAAA	59.566	38.462	0.00	0.00	32.34	2.29
1659	4981	7.123247	CACATATTTGTTCCCCTCTCAGAAAAT	59.877	37.037	0.00	0.00	32.34	1.82
1660	4982	7.340487	ACATATTTGTTCCCCTCTCAGAAAATC	59.660	37.037	0.00	0.00	29.55	2.17
1662	4984	2.637872	TGTTCCCCTCTCAGAAAATCGT	59.362	45.455	0.00	0.00	0.00	3.73
1663	4985	3.263261	GTTCCCCTCTCAGAAAATCGTC	58.737	50.000	0.00	0.00	0.00	4.20
1664	4986	2.821437	TCCCCTCTCAGAAAATCGTCT	58.179	47.619	0.00	0.00	0.00	4.18
1767	5129	2.642254	CCTGCCGGTCGTCTTGGTA	61.642	63.158	1.90	0.00	0.00	3.25
1816	5178	5.757320	CCTCATTCTGAGCGTGAAATAGATT	59.243	40.000	0.00	0.00	42.98	2.40
1833	5195	2.076863	GATTATCCCCGCCTTTCGATG	58.923	52.381	0.00	0.00	41.67	3.84
1869	5231	8.542497	TGTAATGATACTGTTGTAACCTGTTC	57.458	34.615	0.00	0.00	32.98	3.18
1870	5232	6.721571	AATGATACTGTTGTAACCTGTTCG	57.278	37.500	0.00	0.00	31.80	3.95
1874	5236	1.790623	CTGTTGTAACCTGTTCGTCCG	59.209	52.381	0.00	0.00	0.00	4.79
1879	5241	2.360483	TGTAACCTGTTCGTCCGTGTAA	59.640	45.455	0.00	0.00	0.00	2.41
1885	5247	2.195096	TGTTCGTCCGTGTAAGTTGTG	58.805	47.619	0.00	0.00	0.00	3.33
1889	5251	1.071814	TCCGTGTAAGTTGTGCCCC	59.928	57.895	0.00	0.00	0.00	5.80
1918	5286	2.558359	CGCAGTTTCATTTCCTTCCCTT	59.442	45.455	0.00	0.00	0.00	3.95
1919	5287	3.005791	CGCAGTTTCATTTCCTTCCCTTT	59.994	43.478	0.00	0.00	0.00	3.11
1920	5288	4.309933	GCAGTTTCATTTCCTTCCCTTTG	58.690	43.478	0.00	0.00	0.00	2.77
1921	5289	4.309933	CAGTTTCATTTCCTTCCCTTTGC	58.690	43.478	0.00	0.00	0.00	3.68
1922	5290	3.324846	AGTTTCATTTCCTTCCCTTTGCC	59.675	43.478	0.00	0.00	0.00	4.52
1938	5306	2.266372	CCCGTTATGCACCGGTCA	59.734	61.111	2.59	6.66	42.67	4.02
2010	5378	5.877564	TGTGCCTTCGATACATGTGAAATTA	59.122	36.000	9.11	0.00	0.00	1.40
2096	5464	9.961266	TTTTCATGTATACGAACGAAAATACAG	57.039	29.630	17.87	13.26	38.00	2.74
2151	5519	7.290110	AGTTCATCTGGATACGTATGAATCA	57.710	36.000	13.97	5.23	39.70	2.57
2156	5524	9.559732	TCATCTGGATACGTATGAATCATTTTT	57.440	29.630	13.97	0.00	42.51	1.94
2170	5538	4.938575	TCATTTTTCCCTAACCTAGCCA	57.061	40.909	0.00	0.00	0.00	4.75
2178	5546	2.901051	CTAACCTAGCCACCGCCACG	62.901	65.000	0.00	0.00	34.57	4.94
2215	5583	1.249407	GCGATCCTCTACCTCCGATT	58.751	55.000	0.00	0.00	0.00	3.34
2224	5592	1.753073	CTACCTCCGATTTACACCGGT	59.247	52.381	0.00	0.00	45.48	5.28
2248	5616	1.704082	CTGGTCCCCTCTACCTCCA	59.296	63.158	0.00	0.00	37.91	3.86
2261	5629	1.073722	CCTCCAACTGCTGCTCCAA	59.926	57.895	0.00	0.00	0.00	3.53
2277	5650	2.529389	AACGGCAAGAGGGAGGGT	60.529	61.111	0.00	0.00	0.00	4.34
2299	5672	2.679342	CCCCATTTCCTCCGCTCCA	61.679	63.158	0.00	0.00	0.00	3.86
2308	5681	1.497716	TCCTCCGCTCCATAGTTAGGA	59.502	52.381	0.00	0.00	0.00	2.94
2333	5706	2.074230	TTTCGTAGGTCGTGGTGCGT	62.074	55.000	0.00	0.00	42.13	5.24
2347	5721	4.612412	GCGTCGTTGGGGTGGTGA	62.612	66.667	0.00	0.00	0.00	4.02
2348	5722	2.109387	CGTCGTTGGGGTGGTGAA	59.891	61.111	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.760799	CATGTGGCCATGTGGGGG	60.761	66.667	9.72	0.00	42.92	5.40
87	88	0.179200	GTTTATGACGCGTGGCCAAG	60.179	55.000	20.70	15.06	0.00	3.61
128	129	1.079127	CCGAGCCGACTCAAACCAT	60.079	57.895	0.00	0.00	43.66	3.55
1203	4431	2.355363	CCGAAGACGAACACGGCA	60.355	61.111	0.00	0.00	42.66	5.69
1458	4686	8.719648	CCGTTACCACAAACATATACTAAAACA	58.280	33.333	0.00	0.00	0.00	2.83
1522	4838	4.223923	CCTGAAACTCTGTTACCATCTCCT	59.776	45.833	0.00	0.00	0.00	3.69
1523	4839	4.020128	ACCTGAAACTCTGTTACCATCTCC	60.020	45.833	0.00	0.00	0.00	3.71
1524	4840	5.153950	ACCTGAAACTCTGTTACCATCTC	57.846	43.478	0.00	0.00	0.00	2.75
1525	4841	5.308237	AGAACCTGAAACTCTGTTACCATCT	59.692	40.000	0.00	0.00	0.00	2.90
1526	4842	5.409826	CAGAACCTGAAACTCTGTTACCATC	59.590	44.000	0.00	0.00	33.39	3.51
1527	4843	5.308825	CAGAACCTGAAACTCTGTTACCAT	58.691	41.667	0.00	0.00	33.39	3.55
1528	4844	4.703897	CAGAACCTGAAACTCTGTTACCA	58.296	43.478	0.00	0.00	33.39	3.25
1577	4893	4.038271	AGGCAAAGACCAGATCAATGAA	57.962	40.909	0.00	0.00	0.00	2.57
1593	4909	1.950828	TTCCGTTCGTAACAAGGCAA	58.049	45.000	0.00	0.00	0.00	4.52
1658	4980	2.564947	ACTGAAGAAAGGCAGAGACGAT	59.435	45.455	0.00	0.00	36.07	3.73
1659	4981	1.964223	ACTGAAGAAAGGCAGAGACGA	59.036	47.619	0.00	0.00	36.07	4.20
1660	4982	2.447244	ACTGAAGAAAGGCAGAGACG	57.553	50.000	0.00	0.00	36.07	4.18
1662	4984	2.231478	CGGTACTGAAGAAAGGCAGAGA	59.769	50.000	0.00	0.00	36.07	3.10
1663	4985	2.028930	ACGGTACTGAAGAAAGGCAGAG	60.029	50.000	9.17	0.00	36.07	3.35
1664	4986	1.968493	ACGGTACTGAAGAAAGGCAGA	59.032	47.619	9.17	0.00	36.07	4.26
1755	5117	1.014564	GTGCAGCTACCAAGACGACC	61.015	60.000	0.00	0.00	0.00	4.79
1767	5129	1.242076	CAAAGGCTACAAGTGCAGCT	58.758	50.000	3.63	0.00	37.91	4.24
1816	5178	0.834612	AACATCGAAAGGCGGGGATA	59.165	50.000	0.00	0.00	41.33	2.59
1854	5216	1.790623	CGGACGAACAGGTTACAACAG	59.209	52.381	0.00	0.00	0.00	3.16
1863	5225	1.790623	CAACTTACACGGACGAACAGG	59.209	52.381	0.00	0.00	0.00	4.00
1869	5231	1.562575	GGGCACAACTTACACGGACG	61.563	60.000	0.00	0.00	0.00	4.79
1870	5232	1.232621	GGGGCACAACTTACACGGAC	61.233	60.000	0.00	0.00	0.00	4.79
1874	5236	0.816421	ACACGGGGCACAACTTACAC	60.816	55.000	0.00	0.00	0.00	2.90
1879	5241	2.515991	CACACACGGGGCACAACT	60.516	61.111	0.00	0.00	0.00	3.16
1889	5251	0.316937	AATGAAACTGCGCACACACG	60.317	50.000	5.66	0.00	0.00	4.49
1918	5286	2.748251	CCGGTGCATAACGGGCAA	60.748	61.111	16.69	0.00	46.08	4.52
1938	5306	1.608590	CGATCCACAAAGGCACAAACT	59.391	47.619	0.00	0.00	37.29	2.66
2113	5481	3.823304	AGATGAACTTTGTTTCCCTCTGC	59.177	43.478	0.00	0.00	0.00	4.26
2114	5482	4.217118	CCAGATGAACTTTGTTTCCCTCTG	59.783	45.833	0.00	0.00	35.75	3.35
2121	5489	7.822334	TCATACGTATCCAGATGAACTTTGTTT	59.178	33.333	4.74	0.00	0.00	2.83
2151	5519	3.623954	CGGTGGCTAGGTTAGGGAAAAAT	60.624	47.826	0.00	0.00	0.00	1.82
2156	5524	2.062177	GCGGTGGCTAGGTTAGGGA	61.062	63.158	0.00	0.00	35.83	4.20
2178	5546	1.908483	CCTCCCTAGTGGCCTTCAC	59.092	63.158	3.32	0.00	46.39	3.18
2186	5554	4.609098	AGGATCGCCTCCCTAGTG	57.391	61.111	0.71	0.00	46.27	2.74
2215	5583	2.589157	CCAGCCCTCACCGGTGTAA	61.589	63.158	32.74	15.11	0.00	2.41
2242	5610	1.708993	TTGGAGCAGCAGTTGGAGGT	61.709	55.000	0.00	0.00	0.00	3.85
2248	5616	2.980233	GCCGTTGGAGCAGCAGTT	60.980	61.111	0.00	0.00	0.00	3.16
2261	5629	3.322466	CACCCTCCCTCTTGCCGT	61.322	66.667	0.00	0.00	0.00	5.68
2277	5650	2.978946	GCGGAGGAAATGGGGTCCA	61.979	63.158	0.00	0.00	37.65	4.02
2299	5672	7.191593	ACCTACGAAACCAAATCCTAACTAT	57.808	36.000	0.00	0.00	0.00	2.12
2308	5681	2.224354	ACCACGACCTACGAAACCAAAT	60.224	45.455	0.00	0.00	45.77	2.32
2333	5706	1.527380	GCTTTCACCACCCCAACGA	60.527	57.895	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.